› 5kn9

X-ray diffraction
1.93Å resolution

MutY N-terminal domain in complex with DNA containing an intrahelical oxoG:A base-pair

Released:
DOI: 10.2210/pdb5kn9/pdb
PDB entry 5kn9 coloured by chain, front view.
PDB entry 5kn9 coloured by chain, side view.
PDB entry 5kn9 coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase.
Wang L, Chakravarthy S, Verdine GL
J Biol Chem 292 5007-5017 (2017)
PMID: 28130451

Function and Biology Details

Reaction catalysed: 
Hydrolyzes free adenine bases from 7,8-dihydro-8-oxoguanine:adenine mismatched double-stranded DNA, leaving an apurinic site.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118959 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Adenine DNA glycosylase Chain: A
Molecule details ›
Chain: A
Length: 232 amino acids
Theoretical weight: 26.69 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: P83847 (Residues: 1-229; Coverage: 63%)
Gene name: mutY
Sequence domains:
Structure domains:
DNA (5'-D(*AP*TP*CP*CP*(8OG)P*GP*TP*GP*CP*T)-3') Chain: C
Molecule details ›
Chain: C
Length: 10 nucleotides
Theoretical weight: 3.05 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided
DNA (5'-D(*AP*GP*CP*AP*CP*AP*GP*GP*AP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 10 nucleotides
Theoretical weight: 3.08 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SF4 1 x SF4
Ligand CA 2 x CA
1 modified residue:
Ligand 8OG 1 x 8OG

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: P21
Unit cell:
a: 49.878Å b: 38.759Å c: 82.96Å
α: 90° β: 105.66° γ: 90°
R-values:
R R work R free
0.172 0.169 0.229
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Computational investigations on target-site searching and recognition mechanisms by thymine DNA glycosylase during DNA repair process.
Wang et al. (2022)
1 more

1 mention without citation

Structural Basis for the Lesion-scanning Mechanism of the MutY DNA Glycosylase.
Wang et al. (2017)